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Genome-wide replication landscape of Candida glabrata.

Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF - BMC Biol. (2015)

Bottom Line: Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata.No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), F-75015, Paris, France. stephane.descorps-declere@pasteur.fr.

ABSTRACT

Background: The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments.

Results: We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.

Conclusions: Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.

No MeSH data available.


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Replication timing of chromosomal arms. a For each chromosome arm, T50 are represented as boxplots. Red: left chromosome arm values; blue: right chromosome arm values. b Phylogeny of C-left and right arm genes. Average Z-scores of distances between C. glabrata genes and closely related yeast species are shown for each chromosome C arm. None of these distances was significantly different from the other (t-test p-values of C left Z-scores Nc vs Kp, 0.93; Nc vs Zr, 0.79; t-test p-values of C right Z-scores Nc vs Kp, 0.90; Nc vs Zr, 0.70; significance threshold 0.05). Kp Kluyveromyces polysporus, Nc Naumovozyma castellii, Zr Zygosaccharomyces rouxii
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Fig4: Replication timing of chromosomal arms. a For each chromosome arm, T50 are represented as boxplots. Red: left chromosome arm values; blue: right chromosome arm values. b Phylogeny of C-left and right arm genes. Average Z-scores of distances between C. glabrata genes and closely related yeast species are shown for each chromosome C arm. None of these distances was significantly different from the other (t-test p-values of C left Z-scores Nc vs Kp, 0.93; Nc vs Zr, 0.79; t-test p-values of C right Z-scores Nc vs Kp, 0.90; Nc vs Zr, 0.70; significance threshold 0.05). Kp Kluyveromyces polysporus, Nc Naumovozyma castellii, Zr Zygosaccharomyces rouxii

Mentions: In order to detect a possible bias toward early or late replication of a chromosome arm, similar to what has been described for L. kluyveri [15], T50 were plotted for each chromosome arm separately. No significant difference was observed between left and right arms, except for three chromosomes, B, C, and G (Fig. 4a). Chromosomes B and G were acrocentric (Fig. 2). Therefore, the observed difference in arm replication timing for these two chromosomes was probably due to the quasi-absence of origins in one arm. For chromosome C, however, the centromere was located three-quarters along the chromosome length, and its right arm replicated earlier. No difference in GC content was detected between left and right arms (Fig. 2), as compared to what was observed for L. kluyveri chromosome C left arm [15], presenting a 10 % GC enrichment and a much earlier replication pattern. Because hybridization between yeast species and large DNA introgressions are very common among yeasts [35, 36], it is possible that the two arms of C. glabrata chromosome C had different origins, explaining their different replication patterns. All chromosome C proteins were extracted and compared to Naumovozyma castellii, Kluyveromyces polysporus, and Zygosaccharomyces rouxii complete proteomes. These three species were chosen because they are the closest sequenced species outside the C. glabrata clade [22]. Proteome comparisons and clustering (“Methods” and Fig. 4b), showed no detectable evidence that C. glabrata chromosome C left and right arm proteins come from different phylogenetic origins. In support of this conclusion, mapping of ancestral centromeres by Gordon et al. [37] showed that C. glabrata CEN3 is an ancestral centromere and synteny is conserved across it, a result hardly compatible with chromosomal fusion of two different chromosomes. It must be concluded that the difference in replication timing observed for these two chromosomal arms is therefore not due to different phylogenetic origins.Fig. 4


Genome-wide replication landscape of Candida glabrata.

Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF - BMC Biol. (2015)

Replication timing of chromosomal arms. a For each chromosome arm, T50 are represented as boxplots. Red: left chromosome arm values; blue: right chromosome arm values. b Phylogeny of C-left and right arm genes. Average Z-scores of distances between C. glabrata genes and closely related yeast species are shown for each chromosome C arm. None of these distances was significantly different from the other (t-test p-values of C left Z-scores Nc vs Kp, 0.93; Nc vs Zr, 0.79; t-test p-values of C right Z-scores Nc vs Kp, 0.90; Nc vs Zr, 0.70; significance threshold 0.05). Kp Kluyveromyces polysporus, Nc Naumovozyma castellii, Zr Zygosaccharomyces rouxii
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Fig4: Replication timing of chromosomal arms. a For each chromosome arm, T50 are represented as boxplots. Red: left chromosome arm values; blue: right chromosome arm values. b Phylogeny of C-left and right arm genes. Average Z-scores of distances between C. glabrata genes and closely related yeast species are shown for each chromosome C arm. None of these distances was significantly different from the other (t-test p-values of C left Z-scores Nc vs Kp, 0.93; Nc vs Zr, 0.79; t-test p-values of C right Z-scores Nc vs Kp, 0.90; Nc vs Zr, 0.70; significance threshold 0.05). Kp Kluyveromyces polysporus, Nc Naumovozyma castellii, Zr Zygosaccharomyces rouxii
Mentions: In order to detect a possible bias toward early or late replication of a chromosome arm, similar to what has been described for L. kluyveri [15], T50 were plotted for each chromosome arm separately. No significant difference was observed between left and right arms, except for three chromosomes, B, C, and G (Fig. 4a). Chromosomes B and G were acrocentric (Fig. 2). Therefore, the observed difference in arm replication timing for these two chromosomes was probably due to the quasi-absence of origins in one arm. For chromosome C, however, the centromere was located three-quarters along the chromosome length, and its right arm replicated earlier. No difference in GC content was detected between left and right arms (Fig. 2), as compared to what was observed for L. kluyveri chromosome C left arm [15], presenting a 10 % GC enrichment and a much earlier replication pattern. Because hybridization between yeast species and large DNA introgressions are very common among yeasts [35, 36], it is possible that the two arms of C. glabrata chromosome C had different origins, explaining their different replication patterns. All chromosome C proteins were extracted and compared to Naumovozyma castellii, Kluyveromyces polysporus, and Zygosaccharomyces rouxii complete proteomes. These three species were chosen because they are the closest sequenced species outside the C. glabrata clade [22]. Proteome comparisons and clustering (“Methods” and Fig. 4b), showed no detectable evidence that C. glabrata chromosome C left and right arm proteins come from different phylogenetic origins. In support of this conclusion, mapping of ancestral centromeres by Gordon et al. [37] showed that C. glabrata CEN3 is an ancestral centromere and synteny is conserved across it, a result hardly compatible with chromosomal fusion of two different chromosomes. It must be concluded that the difference in replication timing observed for these two chromosomal arms is therefore not due to different phylogenetic origins.Fig. 4

Bottom Line: Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata.No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), F-75015, Paris, France. stephane.descorps-declere@pasteur.fr.

ABSTRACT

Background: The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments.

Results: We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.

Conclusions: Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.

No MeSH data available.


Related in: MedlinePlus